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Model Overview

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939

Sequence

UniProt

P19809

Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

STRING

P19809: 574521.E2348C_39

Domain

Link to: [ InterPro ]

	LysM
	Big_2
	Big_1
	Big_1
	Intimin_C
	DUF3442

Model 3D Structure

	Model information:
	Modelled residue range:	566 to 750
	Based on template:	[ 1cwv ]
	Sequence Identity [%]:	25%
	Model date:	2009-12-21
	Revision date:	2009-12-21

Quaternary structure information:	[details]
NA

Ligand information:	[details]
NA

Template Links: [ RCSB ] [ PDBe ] [ SCOP ] [ CATH ]
display model: in [ AstexViewer ]
download model: as [ pdb ] - as [ Deepview project ]

This model has not been updated since 2009-12-21. In the meantime, new template structures may have become available which would allow building a more reliable model. Would you like to submit the target protein to SWISS-MODEL Workspace and build a new model now? [ Submit ]

Alignment


TARGET    566            D KTSAKADGTE AITYTATVKK -NGVAQANVP VSFNIVSGTA
1cwvA     503   ltltaav--i gdgapangkt aitveftvad fegkplagqe vvittnnga-
                                                                      
TARGET                                 sssssssss    sss  ss ssssss    
1cwvA            ssssss  s             sssssssss    sss  ss sssss     


TARGET    606   VLSANSANTN GSGKATVTLK SDKPGQVVVS AKTAEMTSAL NANAVIFVDQ
1cwvA     550   lpnkitektd angvarialt nttdgvtvvt aevegqrqsv d--thfvkgt
                                                                      
TARGET            sssssss    sssssss      ssssss sss  sssss    sss    
1cwvA             sssssss    sssssss      ssssss sss  sssss s  sss   s


TARGET    656   TKASITEIKA DKTTAVANGQ DAITYTVKVM KG-DKPVSNQ EVTFTTTLGK
1cwvA     598   iaadkstlaa vptsiiadgl mastitlelk dtygdpqaga nvafdttlgn
                                                                      
TARGET                ssss s            sssssss             sssssss   
1cwvA           ss    ssss s sssss      ssssssss ss  sss    sssssss  s


TARGET    705   LSNSTEKTDT NGYAKVTLTS TTPGKSLVSA RVSDVAVDVK APEVEF ---
1cwvA     648   m--gvitdhn dgtysaplts ttlgvatvtv kvdgaafsvp svtvnftadp
                                                                      
TARGET                sss   sssssss      sssssss sss sss     sssss    
1cwvA           s  s  sss   ssssssss     sssssss sss sss     ssssss   


TARGET          ---------- ---------- ---------- ---------- ----------
1cwvA     696   ipdagrssft vstpdiladg tmsstlsfvp vdknghfisg mqglsftqng
                                                                      
TARGET                                                                
1cwvA                  sss ss sssss      sssssss ss   sss     ssssssss


TARGET          ---------- ---------- ---------- ---------- ----------
1cwvA     746   vpvsispite qpdsytatvv gnsvgdvtit pqvdtlilst lqkkislfpv
                                                                      
TARGET                                                                
1cwvA           s  sss  ss s  sssssss     ssssss ssss sss     ssssss  


TARGET          ---------- ---------- ---------- ---------- ----------
1cwvA     796   ptltgilvng qnfatdkgfp ktifknatfq lqmdndvann tqyewsssft
                                                                      
TARGET                                                                
1cwvA            sssssss   sss        sss   ssss ssss   hhh hsssssss  


TARGET          ---------- ---------- ---------- ---------- ----------
1cwvA     846   pnvsvndqgq vtityqtyse vavtakskkf psysvsyrfy pnrwiydggr
                                                                      
TARGET                                                                
1cwvA            sssss  ss ssss       ssssssss     sssssss   sssss    


TARGET          ---------- ---------- ---------- ---------- ----------
1cwvA     896   slvssleasr qcqgsdmsav lessratngt rapdgtlwge wgsltayssd
                                                                      
TARGET                                                                
1cwvA               hhhhhh h     ssss s                hhhh h   hh    


TARGET          ---------- ---------- ---------- ---------- -         
1cwvA     946   wqsgeywvkk tstdfetmnm dtgalqpgpa ylafplcals i         
                                                                      
TARGET                                                                
1cwvA              sssssss    sssssss    sss          sssss s

Quality

[ start new quality assessment in Workspace ]

Ligand Modelling Log

no data available!

Oligomer Modelling Log

no data available!

Template Selection

 - Start SMR-Pipeline for:5073cc9bf4a3f67f9a5316402ee6f97a on BC2-cluster at Mon Dec 21 17:14:24
2009 


 - Analyze BLAST summary ... 
 - Blast template search was successfull, number of templates selected for modeling:  1
 - But still uncovered regions of the target sequence detected, go for: HHSEARCH

 - Run HHSearch to detect more templates...
 - Proof template(s) selection compared to previous Repository update
 - Different number of templates selected (old5 vs new:4): model based on new templates
 - Send 4 Templates for modeling

 - @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
 -                                                         ************************
 - 1f00I (658-939) is a 100% match
 -                                                 ****************
 - building model based on 1cwvA (566-750) was successfull 
 -      *****
 - building model based on 1e0gA (61-115) was successfull 
 -                                        *****************************************
 - building model based on 1cwvA (454-938) was successfull 
 - Parameter file for Repository Pipeline
	
   BLAST
    Evalue :                              0.0001
    Minimum Template size for ranking :   25
    Minimum Sequence identity :           60
	
   HHSEARCH
    Evalue :                              0.0001
    Pvalue :                              50
    mact parameter:                       0.3
	
   RANKING
    Minimal number of uncovered target residues to go for HHSEARCH :           50
    Minimal number of uncovered target residues to accept additional model :   25
	
 - Finish SMR-Pipeline for:5073cc9bf4a3f67f9a5316402ee6f97a on BC2-cluster at Mon Dec 21 17:14:24
2009

Template Search

[ start new template identification in Workspace ]

Template Description

Match

Chain

SeqId

1f02:
Not available
[ SMTL ] [ RCSB ] [ PDBe ] [ SCOP ] [ CATH ]

658-939

1f02I

100%

[Model]

1e5u:
Not available
[ SMTL ] [ RCSB ] [ PDBe ] [ SCOP ] [ CATH ]

753-939

1e5uI

100%

2zqk:
Not available
[ SMTL ] [ RCSB ] [ PDBe ] [ SCOP ] [ CATH ]

750-939

2zqkA

48%

1f00:
Not available
[ SMTL ] [ RCSB ] [ PDBe ] [ SCOP ] [ CATH ]

658-939	1f00I	100%	>target ASITEIKADKTTAVANGQDAITYTVKVMKGDKPVSNQEVTFTTTLGKLSNSTEKTDTNGYAKVTLTSTTPGKSLVSARVSDVAVDVKAPEVEFFTTLTIDDGNIEIVGTGVKGKLPTVWLQYGQVNLKASGGNGKYTWRSANPAIASVDASSGQVTLKEKGTTTISVISSDNQTATYTIATPNSLIVPNMSKRVTYNDAVNTCKNFGGKLPSSQNELENVFKAWGAANKYEYYKSSQTIISWVQQTAQDAKSGVASTYDLVKQNPLNNIKASESNAYATCVK >1f00I ASITEIKADKTTAVANGQDAITYTVKVMKGDKPVSNQEVTFTTTLGKLSNSTEKTDTNGYAKVTLTSTTPGKSLVSARVSDVAVDVKAPEVEFFTTLTIDDGNIEIVGTGVKGKLPTVWLQYGQVNLKASGGNGKYTWRSANPAIASVDASSGQVTLKEKGTTTISVISSDNQTATYTIATPNSLIVPNMSKRVTYNDAVNTCKNFGGKLPSSQNELENVFKAWGAANKYEYYKSSQTIISWVQQTAQDAKSGVASTYDLVKQNPLNNIKASESNAYATCVK [Model]
658-939	1f00I	100%	>target ASITEIKADKTTAVANGQDAITYTVKVMKGDKPVSNQEVTFTTTLGKLSNSTEKTDTNGYAKVTLTSTTPGKSLVSARVSDVAVDVKAPEVEFFTTLTIDDGNIEIVGTGVKGKLPTVWLQYGQVNLKASGGNGKYTWRSANPAIASVDASSGQVTLKEKGTTTISVISSDNQTATYTIATPNSLIVPNMSKRVTYNDAVNTCKNFGGKLPSSQNELENVFKAWGAANKYEYYKSSQTIISWVQQTAQDAKSGVASTYDLVKQNPLNNIKASESNAYATCVK >1f00I ASITEIKADKTTAVANGQDAITYTVKVMKGDKPVSNQEVTFTTTLGKLSNSTEKTDTNGYAKVTLTSTTPGKSLVSARVSDVAVDVKAPEVEFFTTLTIDDGNIEIVGTGVKGKLPTVWLQYGQVNLKASGGNGKYTWRSANPAIASVDASSGQVTLKEKGTTTISVISSDNQTATYTIATPNSLIVPNMSKRVTYNDAVNTCKNFGGKLPSSQNELENVFKAWGAANKYEYYKSSQTIISWVQQTAQDAKSGVASTYDLVKQNPLNNIKASESNAYATCVK [Model]
559-738	1f00I	25%	>target -GVTDFTADKTSAKADGTEAITYTATVKKNGVAQANVPVSFNIVSGTAVLSANSANTNGSGKATVTLKSDKPGQVVVSAKTAEMTSALNANAVIFVDQTKASITEIKADKTTAVANGQDAI----TYTVKVMKGDKPVSNQEVTFTTTLGKLSNSTEKTDT-NGYAKVTLTSTTPGKSLVSARVSD--------------------------------------------------------------------------------------------------------------- >1f00I ASITEIKADKTTAVANGQDAITYTVKVMKGDKPVSNQEVTFTTTLG--KLSNSTEKTDTNGYAKVTLTSTTPGKSLVSARVSDVAVDVKAPEVEFFTTL--TIDDGNIEIVGTGVKGKLPTVWLQYGQVNLKASG---GNGKYTWRSANPA----IASVDASSGQVTL----KEKGTTTISVISSDNQTATYTIATPNSLIVPNMSKRVTYNDAVNTCKNFGGKLPSSQNELENVFKAWGAANKYEYYKSSQTIISWVQQTAQDAKSGVASTYDLVKQNPLNNIKASESNAYATCVK [Model]

1e0g:
Not available
[ SMTL ] [ RCSB ] [ PDBe ] [ SCOP ] [ CATH ]

61-115

1e0gA

16%

1cwv:
Not available
[ SMTL ] [ RCSB ] [ PDBe ] [ SCOP ] [ CATH ]

454-938	1cwvA	16%	>target --LSLNIPHDINGTER-STQKIQLIVKSKYG--L--DRIVWDDS--ALRSQGGQIQHSGSQSAQDYQAILPAYVQGGSNVYKVTARAYDRNGNSSNNVLLTITVLSNGQVVDQVGVTDFTADKTSAKADGTEAITYTATVKK-NGVAQANVPVSFNIVSGTAVLSANSANTNGSGKATVTLKSDKPGQVVVSAKTAEMTSALNANAVIFVDQTK--ASITEIKADKTTAVANGQDAITYTVKVMK-GDKPVSNQEVTFTTTLGKLSNSTEKTDTNGYAKVTLTSTTPGKSLVSARVSDVAVDVKAPEVEFFTTLTIDDGNIEIVGTGVKGKLPTVWLQYGQVNLKAS---GGNGKYTWRSANPAIASVDASSGQVTLKEKGTT--TISVISS--DNQTATYTIATPNSLIVPNMSKRVTYNDAVNTCKNFGGKLPSS--------QNELENVFKAWGAANKYEYYKSSQTIISWVQQTAQDAKSGVASTYDLVKQNPLNNIKASESNAYATCV--- >1cwvA LTLTAAVIGDGAPANGKTAITVEFTVADFEGKPLAGQEVVITTNNGALPNKITEK----TDANGVARIALTNTTD---GVTVVTAEVEGQRQ----SVDTHFVK--GTI---AADKSTLAAVPTSIIADGLMASTITLELKDTYGDPQAGANVAFDTTLGNMG----VITDHNDGTYSAPLTSTTLGVATVTVKVDGAAFSVPSVTVNFTADPIPDAGRSSFTVSTPDILADGTMSSTLSFVPVDKNGHFISGMQGLSFTQNGVPVSISPITEQPDSYTATVVGNSVGDVTITPQVDTLILSTLQKKISLFPVPTLTGILVNGQNFATDKGFPKTIFKNATFQLQMDNDVANNTQYEWSSSFTPNVSVN-DQGQVTITYQTYSEVAVTAKSKKFPSYSVSYRFY-PNRWIYDGGRSLVSSLEASRQCQGSDMSAVLESSRATNGTRAPDGTLWGEWGSLTAYSS--DWQSGEYWVKKTSTD-----FETMNMDTGALQPG---PAYLAFPLCALSI [Model]
566-750	1cwvA	26%	>target -------DKTSAKADGTEAITYTATVKK-NGVAQANVPVSFNIVSGTAVLSANSANTNGSGKATVTLKSDKPGQVVVSAKTAEMTSALNANAVIFVDQTKASITEIKADKTTAVANGQDAITYTVKVMK-GDKPVSNQEVTFTTTLGKLSNSTEKTDTNGYAKVTLTSTTPGKSLVSARVSDVAVDVKAPEVEF------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- >1cwvA LTLTAAVIGDGAPANGKTAITVEFTVADFEGKPLAGQEVVITTNNGA-LPNKITEKTDANGVARIALTNTTDGVTVVTAEVEGQRQSVD--THFVKGTIAADKSTLAAVPTSIIADGLMASTITLELKDTYGDPQAGANVAFDTTLGNM--GVITDHNDGTYSAPLTSTTLGVATVTVKVDGAAFSVPSVTVNFTADPIPDAGRSSFTVSTPDILADGTMSSTLSFVPVDKNGHFISGMQGLSFTQNGVPVSISPITEQPDSYTATVVGNSVGDVTITPQVDTLILSTLQKKISLFPVPTLTGILVNGQNFATDKGFPKTIFKNATFQLQMDNDVANNTQYEWSSSFTPNVSVNDQGQVTITYQTYSEVAVTAKSKKFPSYSVSYRFYPNRWIYDGGRSLVSSLEASRQCQGSDMSAVLESSRATNGTRAPDGTLWGEWGSLTAYSSDWQSGEYWVKKTSTDFETMNMDTGALQPGPAYLAFPLCALSI [Model]
460-736	1cwvA	15%	>target -----------------------------------------------------------------------------------------------------------HDINGTERSTQKIQLIVKSKYGL----DRIVWDDSALRSQGGQIQHSGSQSAQDYQAILPAYVQGGSNVYKVTARAYDRNGNSSNNVLLTITVLSNGQVVDQVGVTDFTADKTSAKADGTEAITYTATVKK-NGVAQANVPVSFNIVSGTAVLSANSANTNGSGKATVTLKSDKPGQVVVSAKTAEMTSALNANAVIFVDQTKASITEIKADKTTAVANGQDAI----TYTVKVMKGDKPVSNQEVTFTTTLGKLSNSTEKTDTNGYAKVTLTSTTPGKSLVSARV------------------------------------------------------------------------------------------------------------------ >1cwvA LTLTAAVIGDGAPANGKTAITVEFTVADFEGKPLAGQEVVITTNNGALPNKITEKTDANGVARIALTNTTDGVTVVTAEVEGQRQSVDTHFVKGTIAADKSTLAAVPTSIIADGLMASTITLELKDTYGDPQAGANVAFDTT-----LGNMGVITDHNDGTYSAPLTSTTLG---VATVTVKVDGAAFSV-PSVTVNFTADPI----PDAGRSSFTVSTPDILADGTMSSTLSFVPVDKNGHFISGMQGLSFTQNGVP--VSISPITEQPDSYTATVVGNSVGDVTITPQVDTLILSTLQKKISLFPV--PTLTGILVNGQNFATDKGFPKTIFKNATFQLQMDNDVANNTQYEWSSSFTP----NVSVNDQGQVTI--TYQTYSEVAVTAKSKKFPSYSVSYRFYPNRWIYDGGRSLVSSLEASRQCQGSDMSAVLESSRATNGTRAPDGTLWGEWGSLTAYSSDWQSGEYWVKKTSTDFETMNMDTGALQPGPAYLAFPLCALSI [Model]

Downloads

download model.tgz

Reference

If you are using models from the SWISS-MODEL Repository, please cite the following articles:

- Kiefer F, Arnold K, Künzli M, Bordoli L, Schwede T (2009).
The SWISS-MODEL Repository and associated resources.
Nucleic Acids Res. 37, D387-D392.

- Jürgen Kopp and Torsten Schwede (2004)
The SWISS-MODEL Repository of annotated three-dimensional protein structure homology models.
Nucleic Acids Res. 32, D230-D234.